eDITH-thur

MATLAB code and data supporting Carraro L, Mächler E, Wüthrich R, Altermatt F. Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems, Nature Communications (accepted), 2020.

Main scripts

• ANALYZE_DATA.m: analyzes data and produces figures and tables shown in the manuscript and extended data.
• MAIN_MCMC.m: calibrates the eDITH model for all 50 genera with data from all 61 sites. Results from this script are stored in results/all.
• MAIN_MCMC_subsampling.m: calibrates the eDITH model for all 50 genera with data from subsets of the overall sampling sites. Results from this script are stored in results/subsampling_....

Folders

• additional_scripts: contains additional scripts called by the main scripts.
  • BuildCovariateMatrix.m: evaluates morphological, geological and land cover covariates. Its results are stored in data/Covariates.m.
  • cmap_DTM.m: defines terrain colormap.
  • CreateNetwork.m: extracts the river network and calculates morphological properties. Its results are stored in results/ThurData.m.
  • hydrology.m: calculates hydrological properties of the catchment. Its results are stores in results/ThurHydrology.m.
  • RegioCov.m: evaluates geographical covariates.
• data: contains data required by the scripts.
  • Clipped_Geology.asc: raster map of geological classes covering the area of interest (processed via ArcGIS, based on data from the Swiss Federal Institute of Topography, accessible at https://www.geocat.ch/geonetwork/srv/eng/md.viewer#/full_view/ca917a71-dcc9-44b6-8804-823c694be516/tab/complete).
  • colZissou.mat: colormap for Figure 5.
  • Covariates.mat: covariate matrix (obtained via additional_scripts/BuildCovariateMatrix.m).
  • DTM.asc: digital terrain model of the area of interest (processed via ArcGIS, based on data from the Swiss Federal Institute of Topography: https://www.geocat.ch/geonetwork/srv/eng/md.viewer#/full_view/7f6ba579-1917-4868-966a-ba91ac157612/tab/complete).
  • DTMad8.asc: raster map of drainage areas (obtained via Taudem subroutine run on ArcGIS).
  • DTMfel.asc: pit-filled digital terrain model (obtained via Taudem subroutine run on ArcGIS).
  • DTMp.asc: flow direction matrix (obtained via Taudem subroutine run on ArcGIS).
  • GenusData.m: eDNA and kicknet data. Data obtained as reported in Mächler et al., 2019 (https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.33).
  • landcover.asc: raster map of land cover classes covering the area of interest (processed via ArcGIS, based on data from the Swiss Federal Institute of Topography, accessible at https://www.geocat.ch/geonetwork/srv/eng/md.viewer#/full_view/cfbd4793-4225-4743-942b-d9b97acfbfcc/tab/complete).
  • SitesFunWorks_coordinates.xlsx: coordinates of sites where eDNA and kicknet sampling were performed.
  • StageDischarge.xlsx: stage-discharge relationships (provided by the Swiss Federal Office for the Environment, available at https://www.hydrodaten.admin.ch/en/2181.html; https://www.hydrodaten.admin.ch/en/2303.html; https://www.hydrodaten.admin.ch/en/2305.html; https://www.hydrodaten.admin.ch/en/2374.html; https://www.hydrodaten.admin.ch/en/2414.html).
  • ThurData.m: data on the catchment morphology and river network extraction (produced by additional_scripts/CreateNetwork.m).
  • ThurHydrology.m: data on hydrological variables across the catchment (produced by additional_scripts/hydrology.m).
  • ThurQ_jun2016.xlsx: discharge time series (provided by the Swiss Federal Office for the Environment, available at https://www.hydrodaten.admin.ch/en/2181.html; https://www.hydrodaten.admin.ch/en/2303.html; https://www.hydrodaten.admin.ch/en/2305.html; https://www.hydrodaten.admin.ch/en/2374.html; https://www.hydrodaten.admin.ch/en/2414.html).
• functions: MATLAB functions required by the scripts.
  • DrawRiverMap.m: draws thematic river maps.
  • eval_accuracy.m: evaluates the accuracy of eDITH predictions with respect to kicknet data.
  • eval_likelihood.m: evaluates likelihood, given a set of parameters and read number data for a given genus.
  • eval_model.m: runs the eDITH model.
  • GOF_NBtest.m: performs the goodness-of-fit test.
  • multiple_boxplot.m: draws multiple boxplots on the same figure. Copied from: Ander Biguri (2020). multiple_boxplot.m https://www.mathworks.com/matlabcentral/fileexchange/47233-multiple_boxplot-m), MATLAB Central File Exchange. Retrieved June 22, 2020.
  • neigh.m: transforms D8 flow direction values in row/column movements.
  • v2struct.m: assembles and disassembles MATLAB structures (used to import data into functions). Copied from: Adi Navve (2020). Pack & Unpack variables to & from structures with enhanced functionality (https://www.mathworks.com/matlabcentral/fileexchange/31532-pack-unpack-variables-to-from-structures-with-enhanced-functionality), MATLAB Central File Exchange. Retrieved June 22, 2020.
• results: stores results produced by scripts MAIN_MCMC.m and MAIN_MCMC_subsampling.m.
  • all: results produced by MAIN_MCMC.m. Files' names correspond to the genera.
  • subsampling_X_Y: results produced by MAIN_MCMC_subsampling.m, where X is the number of validation sites and Y the run number. Files' names correspond to the genera.
  • subsampling_results.m: synthesis of results from subsampling_X_Y.